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Coexpression cluster:C432: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002371!2.32e-18!80;UBERON:0001474!1.16e-15!86;UBERON:0002390!4.11e-15!102;UBERON:0003061!4.11e-15!102;UBERON:0002193!8.92e-14!112;UBERON:0004765!3.69e-13!101;UBERON:0001434!3.69e-13!101;UBERON:0002405!2.31e-12!115;UBERON:0002204!1.06e-11!167;UBERON:0003081!2.32e-10!216;UBERON:0002384!8.28e-09!375
|ontology_enrichment_uberon=UBERON:0002371!2.32e-18!80;UBERON:0001474!1.16e-15!86;UBERON:0002390!4.11e-15!102;UBERON:0003061!4.11e-15!102;UBERON:0002193!8.92e-14!112;UBERON:0004765!3.69e-13!101;UBERON:0001434!3.69e-13!101;UBERON:0002405!2.31e-12!115;UBERON:0002204!1.06e-11!167;UBERON:0003081!2.32e-10!216;UBERON:0002384!8.28e-09!375
|tfbs_overrepresentation=0.705141,0.370939,0.99933,0.312596,0.818862,0.925887,0.286108,0.983505,0.225122,0.180986,0.683731,0.858832,0.79889,0.643817,0.708895,0.387308,0.688098,0.54727,0.340514,0.219007,0.798631,0.663925,0.480948,0.534399,0.277858,0.844435,0.834918,0.51767,0.695713,0.528337,0.827676,0.604798,0.130209,0.833066,0.410089,0.491667,0.999868,0.285884,0.625856,0.410956,0.5406,0.173908,0.685463,0.789681,0.627697,0.246489,0.257064,0.784672,0.595249,0.628619,0.722737,0.34757,0.427497,0.526841,0.817161,0.259426,0.581692,0.840154,0.4649,0.574878,0.204685,0.710825,0.585794,0.454235,0.349628,0.327796,0.964192,0.377773,0.498439,0.753738,0.706286,0.415651,0.510774,0.622687,0.0559081,0.123985,0.540654,0.290028,0.25251,0.0542767,0.537273,0.860976,0.283201,0.607527,0.928646,0.891861,0.399424,0.83434,0.993864,0.391535,0.497109,0.322891,0.536306,0.310703,0.495555,0.608143,0.998818,0.721629,0.525843,0.914246,0.364853,0.916123,0.690572,0.25142,0.849819,0.274132,0.412331,0.957724,0.696991,0.909798,0.786858,0.232931,0.711177,0.127857,0.558762,0.23144,0.145755,0.360548,0.682599,0.488966,0.752958,0.843239,0.6857,0.497219,0.563062,0.775221,0.517533,0.107977,0.491191,0.670858,0.37558,0.449173,0.36346,0.161981,0.643238,0.584005,0.401994,0.353661,0.227084,0.0299268,0.161914,0.648873,0.825958,0.727541,0.96944,0.423481,0.549655,0.490624,0.262525,0.627425,0.82039,0.695522,0.783057,0.186616,0.284398,0.616623,0.448829,0.862994,0.334334,0.231273,0.862085,0.535914,0.613591,0.706553,0.913655,0.605609,0.268915,0.64814,0.270793,0.943193,0.78097,0.678918,0.951498,0.347337,0.47202,0.515052,0.68629,0.785289,0.444504,0.242839,0.734507,0.632722,0.191882,0.609993,0.444086,0.620923,0.787719,0.269752,0.484805,0.768111,0.580576,0.796071,0.6342,0.863575,0.60007,0.309034,0.464583,0.379177,0.415515,0.589595,0.511868,0.379745,0.21345,0.380785,0.675262,0.899978,0.913748,0.717106,0.8299,0.778233,0.302299,0.570429,0.628466,0.600861,0.9435,0.758243,0.747201,0.557713,0.392768,0.565377,0.690727,0.971905,0.727696,0.739742,0.444708,0.645792,0.68212,0.498021,0.380024,0.3772,0.998444,0.975871,0.279407,0.456742,0.538416,0.527638,0.30989,0.903723,0.745571,0.843384,0.786603,0.962776,0.54803,0.485762,0.612384,0.676375,0.478922,0.596521,0.972026,0.614881,0.735009,0.791933,0.793062,0.546605,0.54684,0.736508,0.580924,0.822468,0.424744,0.96275,0.387416,0.771401,0.745279,0.650382,0.236067,0.476994,0.477413,0.523109,0.618379,0.452279,0.917997,0.394242,0.895075,0.989309,0.500614,0.257237,0.65672,0.964014,0.915071,0.997139,0.996215,0.987133,0.999176,0.999955,0.956397,0.999506,0.902175,0.989241,0.69498,0.941358,0.994394,0.953966,0.979006,0.953364,0.980539,0.999346,0.91226,0.929282,0.981509,0.979386,0.998747,0.969706,0.795983,0.968414,0.785085,0.985433,0.590705,0.954067,0.848696,0.986014,0.973404,0.991516,0.996969,0.996853,0.996445,0.869486,0.916755,0.993781,0.893771,0.916661,0.936334,0.993524,0.946156,0.856206,0.995317,0.999164,0.724462,0.944853,0.998651,0.928941,0.989506,0.98957,0.983986,0.929802,0.993026,0.988195,0.972387,0.989728,0.999252,0.786399,0.99546,0.999998,0.999974,0.915346,0.873625,0.466815,0.961588,0.980778,0.911356,0.995458,0.995305,0.974092,0.996519,0.643381,0.920765,0.992568,0.744971,0.412628,0.441175,0.791207,0.999052,0.998822,0.990393,0.983129,0.970547,0.997685,0.997863,0.941646,0.849132,0.943645,0.999889,0.298032,0.4488,0.863834,0.999682,0.998912,0.995238,0.931207,0.960211,0.993083,0.926991,0.952036,0.999851,0.917729,0.999955,0.986319,0.862601,0.956843,0.815127,0.728314,0.99838,0.984939,0.961318,0.98477,0.974982,0.999995,0.956237,0.698594,0.700561,0.886824,0.973163,0.989393,0.991112,0.8923,0.719224,0.306239,0.677121,0.899797,0.670437,0.548746,0.983488,0.930456,0.92328,0.960407,0.770051,0.939071,0.999135,0.902678,0.996564,0.923309,0.903171,0.967124,0.86007,0.981552,0.984039,0.860453,0.991717,0.999745,0.829774,0.9967,0.999691,0.934064,0.909704,0.825805,0.997891,0.920637,0.690252,0.946366,0.919618,0.736371,0.876285,0.971847,0.86817,0.800299,0.511195,0.375501,0.977721,0.995406,0.962026,0.981785,0.963163,0.992853,0.98122,0.99961,0.999513,0.94573,0.425621,0.355482,0.805952,0.463449,0.365276,0.697276,0.856048,0.825509,0.988722,0.988542,0.804534,0.597508,0.736193,0.289141,0.937409,0.645378,0.670622,0.579657,0.913516,0.391761,0.882152,0.129386,0.76511,0.919246,0.977508,0.305745,0.172542,0.606632,0.571171,0.51454,0.501059,0.736884,0.580452,0.290992,0.0294438,0.636297,0.653628,0.836475,0.808024,0.961612,0.325009,0.484917,0.410912,0.786029,0.59523,0.850253,0.955065,0.811493,0.662804,0.798744,0.31516,0.819222,0.981566,0.649342,0.772851,0.790602,0.758637,0.505008,0.535715,0.0831241,0.854679,0.580208,0.915251,0.0363147,0.768427,0.688479,0.83841,0.208692,0.660864,0.294734,0.337897,0.834072,0.720506,0.471391,0.544257,0.737648,0.636087,0.517371,0.356122,0.921643,0.996268,0.677792,0.106633,0.406066,0.838648,0.851943,0.472971,0.453517,0.741578,0.807185,0.351389,0.463331,0.358096,0.278964,0.236241,0.262123,0.894968,0.761017,0.821054,0.319097,0.771019,0.971201,0.227285,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}}
}}

Revision as of 19:55, 8 August 2012


Full id: C432_CD14_choriocarcinoma_Peripheral_CD34_Mast_Fibroblast_granulocyte



Phase1 CAGE Peaks

Hg19::chr12:12605663..12605676,+p@chr12:12605663..12605676
+
Hg19::chr12:12605695..12605708,+p@chr12:12605695..12605708
+
Hg19::chr12:82194544..82194548,+p@chr12:82194544..82194548
+
Hg19::chr12:82204256..82204263,+p@chr12:82204256..82204263
+
Hg19::chr16:86018820..86018823,-p@chr16:86018820..86018823
-
Hg19::chr18:3625092..3625104,+p@chr18:3625092..3625104
+
Hg19::chr1:236021384..236021389,+p@chr1:236021384..236021389
+
Hg19::chr1:94344048..94344055,-p@chr1:94344048..94344055
-
Hg19::chr3:171528432..171528445,-p5@PLD1
Hg19::chr3:197798851..197798882,-p@chr3:197798851..197798882
-
Hg19::chr3:197820053..197820077,-p@chr3:197820053..197820077
-
Hg19::chr5:171837860..171837871,+p@chr5:171837860..171837871
+
Hg19::chr5:65030399..65030409,+p@chr5:65030399..65030409
+
Hg19::chr5:77581386..77581396,+p@chr5:77581386..77581396
+
Hg19::chr5:77583788..77583798,-p@chr5:77583788..77583798
-
Hg19::chr8:133846294..133846325,+p@chr8:133846294..133846325
+
Hg19::chr8:133847581..133847588,-p@chr8:133847581..133847588
-
Hg19::chr8:133847743..133847756,+p@chr8:133847743..133847756
+
Hg19::chr8:29693127..29693132,-p@chr8:29693127..29693132
-
Hg19::chr8:39801800..39801807,+p@chr8:39801800..39801807
+
Hg19::chr8:39807228..39807234,-p@chr8:39807228..39807234
-
Hg19::chr9:15298766..15298791,+p@chr9:15298766..15298791
+
Hg19::chr9:15306169..15306172,+p@chr9:15306169..15306172
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
myeloid leukocyte3.01e-2276
classical monocyte2.42e-2145
CD14-positive, CD16-negative classical monocyte3.95e-2142
granulocyte monocyte progenitor cell8.65e-2171
macrophage dendritic cell progenitor1.29e-1865
myeloid lineage restricted progenitor cell1.08e-1770
monopoietic cell1.79e-1763
monocyte1.79e-1763
monoblast1.79e-1763
promonocyte1.79e-1763
myeloid cell1.17e-14112
common myeloid progenitor1.17e-14112
leukocyte5.44e-13140
multi fate stem cell4.52e-12430
somatic stem cell1.28e-11436
stem cell2.51e-11444
animal cell6.94e-10679
eukaryotic cell6.94e-10679
hematopoietic lineage restricted progenitor cell2.05e-09124
hematopoietic stem cell3.32e-09172
angioblastic mesenchymal cell3.32e-09172
nongranular leukocyte7.69e-09119
connective tissue cell1.02e-08365
mesenchymal cell1.42e-08358
hematopoietic oligopotent progenitor cell1.91e-08165
hematopoietic multipotent progenitor cell1.91e-08165
hematopoietic cell1.01e-07182
motile cell3.53e-07390
somatic cell5.06e-07591
Uber Anatomy
Ontology termp-valuen
bone marrow2.32e-1880
bone element1.16e-1586
hematopoietic system4.11e-15102
blood island4.11e-15102
hemolymphoid system8.92e-14112
skeletal element3.69e-13101
skeletal system3.69e-13101
immune system2.31e-12115
musculoskeletal system1.06e-11167
lateral plate mesoderm2.32e-10216
connective tissue8.28e-09375


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.